The vote went ahead even though many of the 400,000 ethnic Uzbeks forced to flee have not returned.
"People are hoping this parliamentary system will eventually bring stability and security to Kyrgyzstan"
Roza Otunbayeva, the interim president, said she now would be inaugurated as a caretaker president and form her government.
Its members will form a legislative assembly which will pass the necessary laws until parliamentary elections in October.
Tolkun Umaraliev, a blogger for a central Asian blogging network from Bishkek, told Al Jazeera the draft constitution "shifts the country from the presidential system to parliamentary system.
"We have already had two failing presidential systems. As a result people have decided to give the parliamentary system a try this time. People are hoping this parliamentary system will eventually bring stability and security to Kyrgyzstan, and that power will not be around one person or one clan."
Earlier, Otunbayeva declared the referendum a success. "Today is a very important, historic day for the country. The people have put a full stop on the epoch of authoritarian, nepotistic management," she said on Sunday.
The new constitution would make Kyrgyzstan Central Asia's first parliamentary republic.
There were no major reports of violence or voter fraud.
The OSCE Office for Democratic Institutions and Human Rights (ODIHR) said the high voter turnout showed the resilience of Kyrgyz citizens and their desire to shape the future.
"The citizens of Kyrgyzstan turned out in large numbers to vote for a new, democratic and peaceful future for their country," Boris Frlec, head of the observation mission, said on Monday.
"It is now up to all political forces to work together to improve the electoral framework ahead of the upcoming parliamentary elections and build a democratic society based on respect for human rights and the rule of law."
There had been fears of a low turnout because of simmering unrest in the south, but observers from several international bodies, including the OSCE, said they were pleased with the outcome.
"They seem to support the claims that the turnout today was surprisingly high," Al Jazeera's Clayton Swisher, reporting from Bishkek, the Kyrgyz capital, said.
Authorities said on Saturday that all 75,000 people who fled to neighbouring Uzbekistan during the recent ethnic violence had now returned.
Speaking to Al Jazeera, Edil Baisalov, a former senior interim government official, said: "After the Kyrgyz-Uzbek clashes, it felt wrong to continue with the referendum when hundreds of thousands of our citizens were internally displaced. So I was quite critical of the interim government going ahead with the move.
||Citizens were asked to cast a single yes-or-no vote on three proposals:
||A new constitution, which would reduce the powers of the president and make Kyrgyzstan Central Asia's first parliamentary republic
||The interim government. If endorsed, Roza Otunbayeva will remain interim president until December 31, 2011.
||Abolition of constitutional court, which the interim government claims was heavily influenced by allies of an ousted president.
||The constitutional court's powers will now be transferred to the supreme court.
"The fact that thousands of people are going out to vote is a very positive sign. The people of Kyrgyzstan are determined to keep our sovereignty and our statehood, which is what makes this a great day of hope."
The interim government hung posters around Bishkek in the lead-up to the ballot with slogans like "vote for my country" and "our constitution, to change ourselves and our lives".
Officials even sent a passenger jet to fly over the city, dropping leaflets that urged people to remain peaceful during the vote.
Kyrgyzstan's southern region has been at the centre of the intense fighting that forced tens of thousands of people to flee their homes.
Otunbayeva has said up to 2,000 people may have been killed in the recent ethnic violence.
Investigators on Saturday began exhuming some of the bodies of those killed in the clashes that were not officially identified before being buried.
Bakyt Alynbayev, Kygyzstan's acting deputy interior minster, said the investigation was "in the interests of the victims themselves" and "necessary for settling the issue of compensation".
The violence in June followed an uprising last April that led to the overthrow of Kurmanbek Bakiyev as president and the installation of the provisional government.